from snakemake.utils import min_version

##### set minimum snakemake version #####
# This workflow is tested with snakemake version 8.28.0

min_version("8.25.3")

##### setup config #####
# configfile: "config/config.yaml"


##### load rules #####


include: "rules/common.smk"
include: "rules/ref.smk"
include: "rules/seq.smk"
include: "rules/counts.smk"
include: "rules/align.smk"

##### target rules #####


rule all:
	input:
		get_upstream_output(),
	default_target: True